FMO DATABASE

FMODB ID: K9K23

Calculation Name: 5F4Y-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F4Y

Chain ID: B

ChEMBL ID:

UniProt ID: Q13796

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	150
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1300211.952664
FMO2-HF: Nuclear repulsion	1239519.207141
FMO2-HF: Total energy	-60692.745523
FMO2-MP2: Total energy	-60870.647722

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(B:1426:SER)

Summations of interaction energy for fragment #1(B:1426:SER)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-9.718	-5.493	4.361	-3.9	-4.689	-0.031

Interaction energy analysis for fragmet #1(B:1426:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.042 / q_NPA : -0.026

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	B	1428	LEU	0	0.046	0.011	3.808	-1.837	-0.158	-0.019	-0.768	-0.893	0.002
4	B	1429	ASP	-1	-0.879	-0.944	2.228	-11.387	-9.005	4.381	-3.089	-3.675	-0.033
5	B	1430	HIS	0	0.002	0.005	4.176	1.546	1.710	-0.001	-0.043	-0.121	0.000
6	B	1431	ASP	-1	-0.810	-0.889	5.985	-0.128	-0.128	0.000	0.000	0.000	0.000
7	B	1432	LEU	0	-0.017	-0.008	7.188	0.614	0.614	0.000	0.000	0.000	0.000
8	B	1433	SER	0	-0.007	-0.005	7.926	0.503	0.503	0.000	0.000	0.000	0.000
9	B	1434	VAL	0	-0.041	-0.010	9.705	0.342	0.342	0.000	0.000	0.000	0.000
10	B	1435	LYS	1	0.866	0.910	12.041	1.153	1.153	0.000	0.000	0.000	0.000
11	B	1436	LYS	1	0.866	0.943	11.921	1.101	1.101	0.000	0.000	0.000	0.000
12	B	1437	GLN	0	-0.032	-0.028	13.806	0.096	0.096	0.000	0.000	0.000	0.000
13	B	1438	GLU	-1	-0.903	-0.957	15.688	-0.584	-0.584	0.000	0.000	0.000	0.000
14	B	1439	LEU	0	-0.044	-0.025	17.413	0.090	0.090	0.000	0.000	0.000	0.000
15	B	1440	ILE	0	0.016	0.009	16.296	0.073	0.073	0.000	0.000	0.000	0.000
16	B	1441	GLU	-1	-0.872	-0.919	19.432	-0.430	-0.430	0.000	0.000	0.000	0.000
17	B	1442	SER	0	-0.070	-0.048	21.811	0.061	0.061	0.000	0.000	0.000	0.000
18	B	1443	ILE	0	0.015	0.011	22.611	0.039	0.039	0.000	0.000	0.000	0.000
19	B	1444	SER	0	0.011	0.012	24.036	0.041	0.041	0.000	0.000	0.000	0.000
20	B	1445	ARG	1	0.950	0.968	25.700	0.311	0.311	0.000	0.000	0.000	0.000
21	B	1446	LYS	1	0.941	0.979	27.577	0.224	0.224	0.000	0.000	0.000	0.000
22	B	1447	LEU	0	0.010	0.002	27.020	0.019	0.019	0.000	0.000	0.000	0.000
23	B	1448	GLN	0	-0.032	-0.010	29.671	0.026	0.026	0.000	0.000	0.000	0.000
24	B	1449	VAL	0	0.002	0.003	32.119	0.012	0.012	0.000	0.000	0.000	0.000
25	B	1450	LEU	0	-0.037	-0.015	31.577	0.011	0.011	0.000	0.000	0.000	0.000
26	B	1451	ARG	1	0.807	0.886	31.630	0.201	0.201	0.000	0.000	0.000	0.000
27	B	1452	GLU	-1	-0.920	-0.951	36.016	-0.146	-0.146	0.000	0.000	0.000	0.000
28	B	1453	ALA	0	-0.033	-0.017	37.807	0.009	0.009	0.000	0.000	0.000	0.000
29	B	1454	ARG	1	0.888	0.937	36.185	0.151	0.151	0.000	0.000	0.000	0.000
30	B	1455	GLU	-1	-0.857	-0.940	38.870	-0.132	-0.132	0.000	0.000	0.000	0.000
31	B	1456	SER	0	-0.014	-0.013	42.158	0.006	0.006	0.000	0.000	0.000	0.000
32	B	1457	LEU	0	0.014	0.021	43.431	0.005	0.005	0.000	0.000	0.000	0.000
33	B	1458	LEU	0	-0.030	-0.024	43.839	0.005	0.005	0.000	0.000	0.000	0.000
34	B	1459	GLU	-1	-0.948	-0.957	46.993	-0.077	-0.077	0.000	0.000	0.000	0.000
35	B	1460	ASP	-1	-0.881	-0.943	47.878	-0.086	-0.086	0.000	0.000	0.000	0.000
36	B	1461	VAL	0	-0.055	-0.028	48.236	0.004	0.004	0.000	0.000	0.000	0.000
37	B	1462	GLN	0	0.009	0.023	50.945	0.003	0.003	0.000	0.000	0.000	0.000
38	B	1463	ALA	0	0.013	0.006	53.135	0.004	0.004	0.000	0.000	0.000	0.000
39	B	1464	ASN	0	0.004	-0.018	53.966	0.005	0.005	0.000	0.000	0.000	0.000
40	B	1465	THR	0	-0.051	-0.036	54.374	0.003	0.003	0.000	0.000	0.000	0.000
41	B	1466	VAL	0	-0.058	-0.034	56.888	0.003	0.003	0.000	0.000	0.000	0.000
42	B	1467	LEU	0	0.038	0.034	58.555	0.002	0.002	0.000	0.000	0.000	0.000
43	B	1468	GLY	0	0.035	-0.001	59.308	0.002	0.002	0.000	0.000	0.000	0.000
44	B	1469	ALA	0	-0.049	-0.032	60.843	0.002	0.002	0.000	0.000	0.000	0.000
45	B	1470	GLU	-1	-0.936	-0.958	63.179	-0.049	-0.049	0.000	0.000	0.000	0.000
46	B	1471	VAL	0	0.029	0.007	63.235	0.002	0.002	0.000	0.000	0.000	0.000
47	B	1472	GLU	-1	-0.923	-0.949	64.659	-0.048	-0.048	0.000	0.000	0.000	0.000
48	B	1473	ALA	0	-0.035	-0.027	66.522	0.002	0.002	0.000	0.000	0.000	0.000
49	B	1474	ILE	0	0.028	0.017	67.802	0.002	0.002	0.000	0.000	0.000	0.000
50	B	1475	VAL	0	0.019	0.002	68.142	0.002	0.002	0.000	0.000	0.000	0.000
51	B	1476	LYS	1	0.785	0.893	68.319	0.047	0.047	0.000	0.000	0.000	0.000
52	B	1477	GLY	0	-0.043	-0.011	72.320	0.001	0.001	0.000	0.000	0.000	0.000
53	B	1478	VAL	0	-0.038	-0.016	73.562	0.001	0.001	0.000	0.000	0.000	0.000
54	B	1479	CYS	0	-0.050	-0.008	73.436	0.001	0.001	0.000	0.000	0.000	0.000
55	B	1480	LYS	1	0.879	0.932	75.526	0.035	0.035	0.000	0.000	0.000	0.000
56	B	1481	PRO	0	0.050	0.005	75.178	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	1482	SER	0	-0.016	-0.004	74.240	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	1483	GLU	-1	-0.809	-0.890	73.097	-0.038	-0.038	0.000	0.000	0.000	0.000
59	B	1484	PHE	0	0.054	0.030	68.711	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	1485	ASP	-1	-0.828	-0.893	69.583	-0.044	-0.044	0.000	0.000	0.000	0.000
61	B	1486	LYS	1	0.923	0.954	68.690	0.038	0.038	0.000	0.000	0.000	0.000
62	B	1487	PHE	0	0.055	0.029	64.676	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	1488	ARG	1	0.875	0.914	65.055	0.044	0.044	0.000	0.000	0.000	0.000
64	B	1489	MET	0	-0.054	-0.030	63.906	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	1490	PHE	0	-0.003	0.007	60.008	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	1491	ILE	0	0.045	0.027	59.832	-0.002	-0.002	0.000	0.000	0.000	0.000
67	B	1492	GLY	0	-0.008	-0.002	59.110	-0.003	-0.003	0.000	0.000	0.000	0.000
68	B	1493	ASP	-1	-0.786	-0.883	58.435	-0.056	-0.056	0.000	0.000	0.000	0.000
69	B	1494	LEU	0	-0.007	0.002	55.091	-0.002	-0.002	0.000	0.000	0.000	0.000
70	B	1495	ASP	-1	-0.746	-0.853	53.422	-0.069	-0.069	0.000	0.000	0.000	0.000
71	B	1496	LYS	1	0.772	0.877	52.711	0.061	0.061	0.000	0.000	0.000	0.000
72	B	1497	VAL	0	0.023	0.010	52.878	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	1498	VAL	0	0.008	0.004	49.377	-0.002	-0.002	0.000	0.000	0.000	0.000
74	B	1499	ASN	0	0.025	0.001	48.663	-0.006	-0.006	0.000	0.000	0.000	0.000
75	B	1500	LEU	0	-0.028	-0.010	48.039	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	1501	LEU	0	-0.007	-0.007	47.235	-0.003	-0.003	0.000	0.000	0.000	0.000
77	B	1502	LEU	0	0.001	-0.003	44.339	-0.003	-0.003	0.000	0.000	0.000	0.000
78	B	1503	SER	0	-0.042	-0.013	43.764	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	1504	LEU	0	-0.114	-0.041	43.916	-0.002	-0.002	0.000	0.000	0.000	0.000
80	B	1505	SER	0	-0.026	-0.005	41.266	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	1538	ILE	0	0.041	0.000	46.559	0.001	0.001	0.000	0.000	0.000	0.000
82	B	1539	GLN	0	0.006	0.007	48.777	0.002	0.002	0.000	0.000	0.000	0.000
83	B	1540	GLN	0	0.032	0.029	49.295	0.000	0.000	0.000	0.000	0.000	0.000
84	B	1541	HIS	0	0.028	0.011	46.079	0.004	0.004	0.000	0.000	0.000	0.000
85	B	1542	GLU	-1	-0.873	-0.937	49.623	-0.063	-0.063	0.000	0.000	0.000	0.000
86	B	1543	ASP	-1	-0.864	-0.934	52.436	-0.059	-0.059	0.000	0.000	0.000	0.000
87	B	1544	ALA	0	-0.028	-0.019	50.952	0.001	0.001	0.000	0.000	0.000	0.000
88	B	1545	LYS	1	0.821	0.900	50.024	0.068	0.068	0.000	0.000	0.000	0.000
89	B	1546	GLU	-1	-0.902	-0.946	53.412	-0.051	-0.051	0.000	0.000	0.000	0.000
90	B	1547	LEU	0	-0.023	-0.020	56.045	0.002	0.002	0.000	0.000	0.000	0.000
91	B	1548	LYS	1	0.846	0.906	52.658	0.070	0.070	0.000	0.000	0.000	0.000
92	B	1549	GLU	-1	-0.924	-0.959	55.846	-0.059	-0.059	0.000	0.000	0.000	0.000
93	B	1550	ASN	0	-0.074	-0.049	58.183	0.003	0.003	0.000	0.000	0.000	0.000
94	B	1551	LEU	0	-0.036	-0.004	56.257	0.002	0.002	0.000	0.000	0.000	0.000
95	B	1552	ASP	-1	-0.766	-0.861	56.829	-0.064	-0.064	0.000	0.000	0.000	0.000
96	B	1553	ARG	1	0.948	0.961	59.905	0.050	0.050	0.000	0.000	0.000	0.000
97	B	1554	ARG	1	0.780	0.880	62.737	0.053	0.053	0.000	0.000	0.000	0.000
98	B	1555	GLU	-1	-0.761	-0.843	60.107	-0.053	-0.053	0.000	0.000	0.000	0.000
99	B	1556	ARG	1	0.816	0.894	62.474	0.053	0.053	0.000	0.000	0.000	0.000
100	B	1557	ILE	0	-0.014	0.004	65.286	0.002	0.002	0.000	0.000	0.000	0.000
101	B	1558	VAL	0	-0.044	-0.030	65.434	0.001	0.001	0.000	0.000	0.000	0.000
102	B	1559	PHE	0	0.021	0.007	65.101	0.001	0.001	0.000	0.000	0.000	0.000
103	B	1560	ASP	-1	-0.883	-0.945	67.116	-0.042	-0.042	0.000	0.000	0.000	0.000
104	B	1561	ILE	0	-0.157	-0.087	70.406	0.002	0.002	0.000	0.000	0.000	0.000
105	B	1562	LEU	0	-0.018	-0.009	66.981	0.001	0.001	0.000	0.000	0.000	0.000
106	B	1563	ALA	0	0.005	0.013	70.091	0.001	0.001	0.000	0.000	0.000	0.000
107	B	1564	ASN	0	-0.107	-0.046	71.447	0.001	0.001	0.000	0.000	0.000	0.000
108	B	1565	TYR	0	-0.044	-0.039	74.011	0.001	0.001	0.000	0.000	0.000	0.000
109	B	1566	LEU	0	-0.038	-0.012	68.841	0.001	0.001	0.000	0.000	0.000	0.000
110	B	1567	SER	0	0.006	0.006	71.523	0.000	0.000	0.000	0.000	0.000	0.000
111	B	1568	GLU	-1	-0.939	-0.984	67.776	-0.047	-0.047	0.000	0.000	0.000	0.000
112	B	1569	GLU	-1	-0.883	-0.939	66.372	-0.048	-0.048	0.000	0.000	0.000	0.000
113	B	1570	SER	0	0.022	0.007	66.167	-0.001	-0.001	0.000	0.000	0.000	0.000
114	B	1571	LEU	0	-0.033	0.002	66.249	-0.001	-0.001	0.000	0.000	0.000	0.000
115	B	1572	ALA	0	0.010	0.005	63.368	-0.002	-0.002	0.000	0.000	0.000	0.000
116	B	1573	ASP	-1	-0.864	-0.934	62.065	-0.055	-0.055	0.000	0.000	0.000	0.000
117	B	1574	TYR	0	-0.110	-0.088	61.574	-0.002	-0.002	0.000	0.000	0.000	0.000
118	B	1575	GLU	-1	-0.843	-0.936	60.960	-0.055	-0.055	0.000	0.000	0.000	0.000
119	B	1576	HIS	0	-0.038	-0.014	55.785	-0.004	-0.004	0.000	0.000	0.000	0.000
120	B	1577	PHE	0	0.016	0.031	56.848	-0.003	-0.003	0.000	0.000	0.000	0.000
121	B	1578	VAL	0	0.036	0.011	56.809	-0.003	-0.003	0.000	0.000	0.000	0.000
122	B	1579	LYS	1	0.935	0.968	52.872	0.070	0.070	0.000	0.000	0.000	0.000
123	B	1580	MET	0	-0.007	-0.009	51.809	-0.004	-0.004	0.000	0.000	0.000	0.000
124	B	1581	LYS	1	0.828	0.921	51.906	0.063	0.063	0.000	0.000	0.000	0.000
125	B	1582	SER	0	-0.061	-0.031	51.766	-0.002	-0.002	0.000	0.000	0.000	0.000
126	B	1583	ALA	0	-0.009	-0.010	48.984	-0.004	-0.004	0.000	0.000	0.000	0.000
127	B	1584	LEU	0	0.054	0.029	47.321	-0.005	-0.005	0.000	0.000	0.000	0.000
128	B	1585	ILE	0	-0.005	0.002	46.413	-0.004	-0.004	0.000	0.000	0.000	0.000
129	B	1586	ILE	0	-0.026	-0.020	44.501	-0.004	-0.004	0.000	0.000	0.000	0.000
130	B	1587	GLU	-1	-0.919	-0.953	42.413	-0.116	-0.116	0.000	0.000	0.000	0.000
131	B	1588	GLN	0	-0.032	-0.030	41.588	-0.004	-0.004	0.000	0.000	0.000	0.000
132	B	1589	ARG	1	0.913	0.963	40.494	0.114	0.114	0.000	0.000	0.000	0.000
133	B	1590	GLU	-1	-0.841	-0.923	38.993	-0.135	-0.135	0.000	0.000	0.000	0.000
134	B	1591	LEU	0	-0.067	-0.025	37.192	-0.013	-0.013	0.000	0.000	0.000	0.000
135	B	1592	GLU	-1	-0.894	-0.943	36.039	-0.131	-0.131	0.000	0.000	0.000	0.000
136	B	1593	ASP	-1	-0.903	-0.943	35.338	-0.149	-0.149	0.000	0.000	0.000	0.000
137	B	1594	LYS	1	0.801	0.885	32.632	0.134	0.134	0.000	0.000	0.000	0.000
138	B	1595	ILE	0	-0.034	-0.022	31.211	-0.017	-0.017	0.000	0.000	0.000	0.000
139	B	1596	HIS	0	-0.030	-0.009	30.723	-0.009	-0.009	0.000	0.000	0.000	0.000
140	B	1597	LEU	0	0.008	0.003	27.615	-0.016	-0.016	0.000	0.000	0.000	0.000
141	B	1598	GLY	0	0.018	0.000	26.697	-0.021	-0.021	0.000	0.000	0.000	0.000
142	B	1599	GLU	-1	-0.815	-0.905	25.720	-0.228	-0.228	0.000	0.000	0.000	0.000
143	B	1600	GLU	-1	-0.849	-0.914	25.509	-0.255	-0.255	0.000	0.000	0.000	0.000
144	B	1601	GLN	0	-0.062	-0.036	22.753	-0.026	-0.026	0.000	0.000	0.000	0.000
145	B	1602	LEU	0	-0.009	-0.006	21.215	-0.049	-0.049	0.000	0.000	0.000	0.000
146	B	1603	LYS	1	0.807	0.897	20.806	0.290	0.290	0.000	0.000	0.000	0.000
147	B	1604	CYS	0	-0.042	-0.024	18.297	-0.012	-0.012	0.000	0.000	0.000	0.000
148	B	1605	LEU	0	-0.063	-0.030	16.751	-0.063	-0.063	0.000	0.000	0.000	0.000
149	B	1606	LEU	0	-0.006	-0.011	15.869	-0.091	-0.091	0.000	0.000	0.000	0.000
150	B	1607	ASP	-1	-0.863	-0.894	14.674	-0.489	-0.489	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1426:SER)